Comparison of two SARS-CoV-2 RT-PCR assays and implication of the instrument software on cycle threshold (Ct) value

The Cycle Threshold (Ct) value of SARS-CoV-2 RT-PCR are used as an indicator of viral load. Using a collection of 45 fresh nasopharyngeal samples collected on universal transport media, we compare the Ct value obtained with 2 RT-PCR assays, the Alinity M SARS-CoV-2 and the Alinity M RESP-4-Plex (Abbott Molecular, Des Plaines, Illinois, Etats-Unis) processed on an Alinity M device. The assays are highly correlated; however, the Ct values were in median lower of 4.54 with the Alinity M RESP-4-Plex. This difference could be attributed to earlier detection of positivity by the software of the Alinity M rather than a difference in RT-PCR performances. The Ct-value of SARS-CoV-2 RT-PCR should be interpreted with caution taking into account the clinical context, pre-analytical and analytical findings.

La valeur du cycle seuil (Ct) des RT-PCR positives pour le SARS-CoV-2 est utilisée pour évaluer si un patient est contagieux. Lors d'un changement de réactif, nous avons comparé les résultats de Ct obtenus pour 45 prélèvements positifs pour le SARS-CoV-2 avec 2 kits de réactifs : Alinity M SARS-CoV-2 et Alinity M RESP-4-Plex (Abbott Molecular, Des Plaines, Illinois, États-Unis) utilisée avec l'automate Alinity M. Les deux méthodes était corrélées mais les Ct étaient en médiane plus bas de 4,54 avec le réactif Alinity M RESP-4-Plex en comparaison du réactif Alinity M SARS-CoV-2. Cette différence semble liée à une détection plus précoce de la positivité par le logiciel de l'Alinity M qu'à une différence de performances. Nous alertons sur le fait que les valeurs de Ct doivent être interprétées avec prudence en prenant en compte le contexte clinique, les limites pré-analytiques et analytiques.

The Panbio COVID-19 Ag Rapid Test: Which Performances are for COVID-19 Diagnosis?

BACKGROUND: Rapid antigen detection assays are promising tools for the diagnosis of COVID-19. We assess the performances of the Panbio COVID-19 Ag Rapid Test. METHODS: The Panbio COVID-19 Ag Rapid test was compared to a reference RT-PCR performed on the same nasopharyngeal swab (NPS). Overall, 81 NPS were tested retrospectively and 330 healthcare workers (HCWs) were tested prospectively. RESULTS: Retrospective analyze. Of the 48 SARS-CoV-2 positive NPS, 19 (39.6%) were found positive with the Panbio COVID-19. There was no cross-reactivity with SARS-CoV-2 negative NPS. The Kappa value was 0.459. Prospective analyze. The prevalence of COVID-19 was 26.1% in symptomatic HCWs. The overall sensitivity and specificity of the Panbio COVID-19 were 47.2% and 100.0% respectively. The sensitivity was 55.2% and 14.3% in those tested within and after 4 days of diseases respectively. CONCLUSIONS: The Panbio COVID-19 Ag Rapid test displays low performance for the identification of SARS-CoV-2 infected patients.

SARS-CoV-2 screening of asymptomatic health care workers: experience of a General hospital.

Health care workers (HCWs) are at major risk to be infected by SARS-CoV-2 and transmit the virus to the patients. Furthermore, travels are a major factor in the diffusion of the virus. We report our experience regarding the screening of asymptomatic HCWs returning from holidays, following the issue of a national guideline on 08/20/2020. The organization of the occupational health department and the clinical laboratory was adapted in order to start the screening on August, 24, 2020. All HCWs tested for SARS-CoV-2 the week before and 4 weeks after the implementation of the screening were included. The mean number of tests was analyzed per working day and working week. Overall, 502 (31.4%) HCWs were tested for SARS-CoV-2 during the study period. The mean number of HCWs tested per working day was 27.1. HCWs accounted for 36.9% (n = 167) and 11.2% (n = 84) of the tests performed in the 1st and the 4th week following the implementation of the guidelines. The number of tests performed each week in HCWs increased by at least 20-fold after the implementation of the guidelines. No asymptomatic HCW was tested positive. Screening of asymptomatic HCWs was poorly effective in the context of low circulation of the virus. We suggest giving priority to infection prevention and control measures and screening of symptomatic subjects and asymptomatic contacts.

An Immunogenicity Report for the Comparison between Heterologous and Homologous Prime-Boost Schedules with ChAdOx1-S and BNT162b2 Vaccines.

BACKGROUND: There is a small amount of immunological data on COVID-19 heterologous vaccination schedules in humans. We assessed the immunogenicity of BNT162b2 (Pfizer/BioNTech) administered as a second dose in healthcare workers primed with ChAdOx1-S (Vaxzevria, AstraZeneca). METHODS: 197 healthcare workers were included in a monocentric observational study in Foch hospital, France, between June and July 2021. The main outcome was the immunogenicity measured by serum SARS-CoV-2 IgG antibodies. RESULTS: 130 participants received the ChAdOx1-S/BNT vaccine and 67 received the BNT/BNT vaccine. The geometric mean of IgG antibodies was significantly higher in the BNT/BNT vaccine group compared to the ChAdOx1-S/BNT vaccine group, namely 10,734.9, 95% CI (9141.1-12,589.3) vs. 7268.6, 95% CI (6501.3-8128.3), respectively (p < 0.001). However, after adjustment for time duration between the prime and second vaccinations, no significant difference was observed (p = 0.181). A negative correlation between antibody levels and time duration between second dose and serology test was observed for the BNT/BNT vaccine (p < 0.001), which remained significant after adjustment for all covariates (p < 0.001), but not for the ChAdOx1-S/BNT vaccine (p = 0.467). CONCLUSIONS: Heterologous and homologous schedules of ChAdOx1-S and BNT vaccines present robust immune responses after the second vaccination. The results observed were equivalent after adjustment for covariates and emphasize the importance of flexibility in deploying mRNA and viral vectored vaccines. Nevertheless, applying the ChAdOx1-S schedule vaccination for the heterologous second dose of BNT was associated with decreased IgG antibody levels compared to the homologous BNT/BNT vaccination.

The Allplex 2019-nCoV (Seegene) assay: which performances are for SARS-CoV-2 infection diagnosis?

Several commercial assays for SARS-CoV-2 RT-PCR are available but few of them were assessed. We evaluate the Allplex 2019-nCoV (Seegene) assay using 41 nasopharyngeal samples. The rates of agreement were 92.7% and 100% with the GeneFinder COVID-19 plus (Elitech) and the diagnosis of the infectious disease specialist respectively. Four samples display a Ct < 22.0 for the E and RdRp genes while the N gene was not detected, suggesting a variability of the viral sequence. There was no cross-reactivity with other respiratory viruses. The Allplex 2019-nCoV appears as a reliable method, but additional evaluations using more samples are needed. RT-PCR assays should probably include at least 2 viral targets.